X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerapintailcommand.cpp;h=9d492afe950713cefd4d1fad7fcd72a6da74640c;hp=3eb6589a83beebf79f8cf812ce519b35d0bcc37e;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0 diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp index 3eb6589..9d492af 100644 --- a/chimerapintailcommand.cpp +++ b/chimerapintailcommand.cpp @@ -14,18 +14,18 @@ //********************************************************************************************************************** vector ChimeraPintailCommand::setParameters(){ try { - CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate); - CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); - CommandParameter pconservation("conservation", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pconservation); - CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pquantile); - CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pfilter); - CommandParameter pwindow("window", "Number", "", "0", "", "", "",false,false); parameters.push_back(pwindow); - CommandParameter pincrement("increment", "Number", "", "25", "", "", "",false,false); parameters.push_back(pincrement); - CommandParameter pmask("mask", "String", "", "", "", "", "",false,false); parameters.push_back(pmask); - CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); - CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave); + CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate); + CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","chimera-accnos",false,true,true); parameters.push_back(pfasta); + CommandParameter pconservation("conservation", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconservation); + CommandParameter pquantile("quantile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pquantile); + CommandParameter pfilter("filter", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfilter); + CommandParameter pwindow("window", "Number", "", "0", "", "", "","","",false,false); parameters.push_back(pwindow); + CommandParameter pincrement("increment", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pincrement); + CommandParameter pmask("mask", "String", "", "", "", "", "","",false,false); parameters.push_back(pmask); + CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir); + CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave); vector myArray; for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } @@ -69,6 +69,22 @@ string ChimeraPintailCommand::getHelpString(){ } } //********************************************************************************************************************** +string ChimeraPintailCommand::getOutputPattern(string type) { + try { + string pattern = ""; + + if (type == "chimera") { pattern = "[filename],[tag],pintail.chimeras-[filename],pintail.chimeras"; } + else if (type == "accnos") { pattern = "[filename],[tag],pintail.accnos-[filename],pintail.accnos"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "ChimeraPintailCommand", "getOutputPattern"); + exit(1); + } +} +//********************************************************************************************************************** ChimeraPintailCommand::ChimeraPintailCommand(){ try { abort = true; calledHelp = true; @@ -76,6 +92,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(){ vector tempOutNames; outputTypes["chimera"] = tempOutNames; outputTypes["accnos"] = tempOutNames; + } catch(exception& e) { m->errorOut(e, "ChimeraPintailCommand", "ChimeraPintailCommand"); @@ -109,6 +126,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option) { vector tempOutNames; outputTypes["chimera"] = tempOutNames; outputTypes["accnos"] = tempOutNames; + //if the user changes the input directory command factory will send this info to us in the output parameter inputDir = validParameter.validFile(parameters, "inputdir", false); @@ -396,13 +414,12 @@ int ChimeraPintailCommand::execute(){ if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it string outputFileName, accnosFileName; - if (maskfile != "") { - outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.chimeras"; - accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + m->getSimpleName(m->getRootName(maskfile)) + ".pintail.accnos"; - }else { - outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "pintail.chimeras"; - accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "pintail.accnos"; - } + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])); + if (maskfile != "") { variables["[tag]"] = m->getSimpleName(m->getRootName(maskfile)); } + outputFileName = getOutputFileName("chimera", variables); + accnosFileName = getOutputFileName("accnos", variables); + if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } @@ -488,7 +505,7 @@ int ChimeraPintailCommand::execute(){ #else //break up file - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) vector positions = m->divideFile(fastaFileNames[s], processors); for (int i = 0; i < (positions.size()-1); i++) { @@ -611,7 +628,7 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string } delete candidateSeq; - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) unsigned long long pos = inFASTA.tellg(); if ((pos == -1) || (pos >= filePos->end)) { break; } #else @@ -619,10 +636,10 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string #endif //report progress - if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } + if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); } } //report progress - if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); } + if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n"); } out.close(); out2.close(); @@ -678,10 +695,10 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi delete candidateSeq; //report progress - if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n"); } + if((i+1) % 100 == 0){ cout << "Processing sequence: " << (i+1) << endl; } } //report progress - if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n"); } + if(num % 100 != 0){ cout << "Processing sequence: " << num << endl; } return 0; @@ -697,7 +714,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi int ChimeraPintailCommand::createProcesses(string outputFileName, string filename, string accnos) { try { -#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) int process = 0; int num = 0;